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Automated ligand fitting with LigandFit

Author(s)
Purpose
Purpose of the LigandFit Wizard
Usage
How the LigandFit Wizard works
How to run the LigandFit Wizard
What the LigandFit wizard needs to run
Specifying which columns of data to use from input data files
Output files from LigandFit
Running from a parameters file
Examples
Sample command_line inputs
Possible Problems
Specific limitations and problems
Literature
Additional information
List of all LigandFit keywords

Author(s)

  • LigandFit Wizard: Tom Terwilliger
  • PHENIX GUI and PDS Server: Nigel W. Moriarty
  • RESOLVE: Tom Terwilliger

Purpose

Purpose of the LigandFit Wizard

The LigandFit Wizard carries out fitting of flexible ligands to electron density maps.

Usage

The LigandFit Wizard can be run from the PHENIX GUI, from the command-line, and from parameters files. All three versions are identical except in the way that they take commands from the user. See Using the PHENIX Wizards for details of how to run a Wizard. The command-line version will be described here.

How the LigandFit Wizard works

The LigandFit wizard provides a command-line and graphical user interface allowing the user to identify a datafile containing crystallographic structure factor information, an optional PDB file with a partial model of the structure without the ligand, and a PDB file containing the ligand to be fit (in an allowed but arbitrary conformation).

The wizard checks the data files for consistency and then calls RESOLVE to carry out the fitting of the ligand into the electron-density map. The map used is normally a difference map, with F=FP-FC. It can also be an Fobs map (calulated from FP with phases PHIC from the input partial model), or an arbitrary map, calculated with FP PHI and FOM. If you supply an input partial model, then the region occupied by the partial model is flattened in the map used to fit the ligand, so that the ligand will normally not get placed in this region.

The ligand fitting is done by RESOLVE in a three-stage process. First, the largest contiguous region of density in the map not already occupied by the model is identified. The ligand will be placed in this density. (If desired, the location of the ligand can instead be defined by the user as near a certain residue or near specified coordinates. ) Next, many possible placements of the largest rigid sub-fragments of the ligand are found within this region of high density. Third, each of these placements is taken as a starting point for fitting the remainder of the ligand. All these ligand fits are scored based on the fit to the density, and the best-fitting placement is written out.

The output of the wizard consists of a fitted ligand in PDB format and a summary of the quality of the fit. Multiple copies of a ligand can be fit to a single map in an automated fashion using the LigandFit wizard as well.

How to run the LigandFit Wizard

Running the LigandFit Wizard is easy. For example, from the command-line you can type:

phenix.ligandfit data=datafile.mtz model=partial_model.pdb ligand=ligand.pdb

The LigandFit Wizard will carry out ligand fitting of the ligand in ligand.pdb based on the structure factor amplitudes in datafile.mtz, calculating phases based on partial-model.pdb. All rotatable bonds will be identified and allowed to take stereochemically reasonable orientations.

What the LigandFit wizard needs to run

The ligandfit wizard needs:

  • (1) a datafile (w1.sca or data=w1.sca); this can be any format

  • (2) a PDB file with your model without ligand (model=partial.pdb; optional if your datafile contains map coefficients)

  • (3) a file with information about your ligand (ligand=side.pdb), or a 3-letter code for your ligand (ligand=ATP)

    The ligand file can be a PDB file with 1 stereochemically acceptable conformation of your ligand. It can alternatively be a file containing a SMILES string, in which case the starting ligand conformation will be generated with the PHENIX elbow routine. It can also be a 3-letter code that specifies a ligand in the Chemical Components Dictionary of the PDB, in which case the ligand is taken from that dictionary with idealized geometry.

    The command_line ligandfit interpreter will guess which file is your data file but you have to tell it which file is the model and which is the ligand.

    Specifying which columns of data to use from input data files

    If one or more of your data files has column names that the Wizard cannot identify automatically, you can specify them yourself. You will need to provide one column "name" for each expected column of data, with "None" for anything that is missing.

    For example, if your data file data.mtz has columns FP SIGFP then you might specify

    data=data.mtz
    input_labels="FP SIGFP"
    

    You can find out all the possible label strings in a data file that you might use by typing:

    phenix.autosol display_labels=data.mtz  # display all labels for data.mtz
    

    You can specify many more parameters as well. See the list of keywords, defaults and descriptions at the end of this page and also general information about running Wizards at Using the PHENIX Wizards for how to do this. Some of the most common parameters are:

    data=w1.sca       # data file
    partial_model=coords.pdb  # starting model without ligand
    ligand=ligand.pdb # any stereochemically allowed conformation of your ligand
    resolution=3     # dmin of 3 A
    quick=False      # specify if you want to look hard for a good conformation
    ligand_cc_min=0.75   # quit if the CC of ligand to map is 0.75 or better
    number_of_ligands=3  # find 3 copies of the ligand
    n_group_search=3     # try 3 different fragments of the ligand in initial search
    ligand_start=side.pdb # build ligand superimposing on side.pdb
    

    Output files from LigandFit

    When you run LigandFit the output files will be in a subdirectory with your run number:

    LigandFit_run_1_/   # subdirectory with results
    

  • A summary file listing the results of the run and the other files produced:
    LigandFit_summary.dat  # overall summary
    

  • A file that lists all parameters and knowledge accumulated by the Wizard during the run (some parts are binary and are not printed)
    LigandFit_Facts.dat   # all Facts about the run
    

  • A warnings file listing any warnings about the run
    LigandFit_warnings.dat  # any warnings
    

  • A PDB file with the fitted ligand (in this case the first copy of ligand number 1):
    ligand_fit_1_1.pdb
    

  • A log file with the fitting of the ligand:
    ligand_1_1.log
    

  • A log file with the fit of the ligand to the map:
    ligand_cc_1_1.log
    

  • Map coefficients for the map used for fitting:
    resolve_map.mtz
    

Running from a parameters file

You can run phenix.ligandfit from a parameters file. This is often convenient because you can generate a default one with:

phenix.ligandfit --show_defaults > my_ligandfit.eff
and then you can just edit this file to match your needs and run it with:
phenix.ligandfit  my_ligandfit.eff

Examples

Sample command_line inputs

  • Standard run of ligandfit (generate map from model and data file)
    phenix.ligandfit w1.sca model=partial.pdb ligand=ATP \
     lig_map_type=fo-fc_difference_map  
    

  • Build into a map from pre-determined coefficients
    phenix.ligandfit data=perfect.mtz \
     lig_map_type=pre_calculated_map_coeffs \
       model=partial.pdb ligand=NAD
    

  • Quick run of ligandfit
    phenix.ligandfit w1.sca model=partial.pdb ligand=ATP quick=True
    

  • Run ligandfit using pre-calculated map coefficients from phenix.refine

    If your refine a model with a command such as,

    phenix.refine data.mtz partial.pdb
    
    then you will end up with the refined model,
    partial_refine_001.pdb
    
    and a map coefficients file:
    partial_refine_001_map_coeffs.mtz
    
    You can then run ligandfit using the 2Fo-Fc map calculated from these map coefficients:
    phenix.ligandfit data=partial_refine_001_map_coeffs.mtz \
     model=partial_refine_001.pdb ligand=NAD quick=True
    
    or if you want to specify the coefficients explicitly you can add the column labels:
    phenix.ligandfit data=partial_refine_001_map_coeffs.mtz  \
    model=partial_refine_001.pdb ligand=GOL quick=True \
    input_labels="2FOFCWT PH2FOFCWT"
    
    For a difference map from the same file you can say:
    phenix.ligandfit data=partial_refine_001_map_coeffs.mtz  \
     model=partial_refine_001.pdb ligand=AMP quick=True \
     input_labels="FOFCWT PHFOFCWT"
    

  • Run ligandfit on a series of ligands specified in ligand_list.dat
    phenix.ligandfit w1.sca model=partial.pdb \
      ligand=ligand_list.dat file_or_file_list=file_with_list_of_files
    
    Note that you have to specify
    file_or_file_list=file_with_list_of_files
    
    or else the Wizard will try to interpret the contents of ligand_list.dat as a SMILES string. Here the "file_with_list_of_files" is a flag, not something you substitute with an actual file name. You use it just as listed above.

  • Place ligand near residue 94 of chain "A" from partial.pdb
    phenix.ligandfit w1.sca model=partial.pdb ligand=ADP \
       ligand_near_chain="A" ligand_near_res=92
    

  • Use start.pdb as a template for some of the atoms in the ligand; build the remainder of the ligand, fixing the coordinates of the corresponding atoms:
    phenix.ligandfit w1.sca model=partial.pdb ligand=GTP \
       ligand_start=start.pdb  
    

  • Use NCS from the model and the first ligand fitted to guess the positions of NCS-related ligands:
    phenix.ligandfit w1.sca model=partial.pdb ligand=GTP \
       ligands_from_ncs=True
    

Possible Problems

Specific limitations and problems

  • The keywords "cell" and "sg" have been replaced with "unit_cell" and "space_group" to make the keywords the same as in other phenix applications.

    • The ligand to be searched for must have at least 3 atoms.

    • The partial-model file must not have any atoms (other than waters, which are automatically removed) in the position where the ligand is to be built. If this file contains atoms other than waters in the position where the ligand is to be built, then you may wish to remove them before building the ligand.

    • If a ring in the ligand can have more than one conformation (e.g., chair or boat conformation) then you need to do separate runs for each conformation of the ring (rings are taken as fixed units in LigandFit).

    • LigandFit ignores insertion codes, so if you specify a residue with ligand_near_res, only the residue number is used.

    • The size of the asymmetric unit in the SOLVE/RESOLVE portion of the LigandFit wizard is limited by the memory in your computer and the binaries used. The Wizard is supplied with regular-size ("", size=6), giant ("_giant", size=12), huge ("_huge", size=18) and extra_huge ("_extra_huge", size=36). Larger-size versions can be obtained on request.

    • The LigandFit Wizard can take most settings of most space groups, however it can only use the hexagonal setting of rhombohedral space groups (eg., #146 R3:H or #155 R32:H), and it cannot use space groups 114-119 (not found in macromolecular crystallography) even in the standard setting due to difficulties with the use of asuset in the version of ccp4 libraries used in PHENIX for these settings and space groups.

    Literature

    Ligand identification using electron-density map correlations. T. C. Terwilliger, P. D. Adams, N. W. Moriarty and J. D. Cohn Acta Cryst. D63, 101-107 (2007)
    [pdf]
    Automated ligand fitting by core-fragment fitting and extension into density. T. C. Terwilliger, H. Klei, P. D. Adams, N. W. Moriarty and J. D. Cohn Acta Cryst. D62, 915-922 (2006)
    [pdf]

    Additional information

    List of all LigandFit keywords

    ------------------------------------------------------------------------------- 
    Legend: black bold - scope names
            black - parameter names
            red - parameter values
            blue - parameter help
            blue bold - scope help
            Parameter values:
              * means selected parameter (where multiple choices are available)
              False is No
              True is Yes
              None means not provided, not predefined, or left up to the program
              "%3d" is a Python style formatting descriptor
    ------------------------------------------------------------------------------- 
    ligandfit
       data= None Datafile. This can be any format if only FP is to be read in. If
             phases are to be read in then MTZ format is required. The Wizard will
             guess the column identification. If you want to specify it you can
             say input_labels="FP" , or input_labels="FP PHIB
             FOM".
       ligand= None Three-letter code of ligand, or file containing information
               about the ligand (PDB or SMILES)
       model= None PDB file with model for everything but the ligand
       quick= False Set to True for running as quickly as possible.
       crystal_info
          unit_cell= None Enter cell parameter a b c alpha beta gamma
          resolution= 0 High-resolution limit. Zero means keep everything.
          space_group= None Space Group symbol (i.e., C2221 or C 2 2 21)
       file_info
          file_or_file_list= *single_file file_with_list_of_files Choose if you
                             want to input a single file with PDB or other
                             information about the ligand or if you want to input
                             a file containing a list of files with this
                             information for a list of ligands
          input_labels= None Labels for input data columns
          lig_map_type= fo-fc_difference_map fobs_map *pre_calculated_map_coeffs 
                       Enter the type of map to use in ligand fitting
                        fo-fc_difference_map: Fo-Fc difference map phased on
                        partial model (requires FOBS in your input file) fobs_map:
                        Fo map phased on partial model (requires FOBS in your
                        input file) pre_calculated_map_coeffs: map calculated from
                        FP PHIB [FOM] coefficients in input data file (or 2FOFCWT
                        PH2FOFCWT coeffs)
          ligand_format= *PDB SMILES Enter whether the files contain SMILES
                         strings or PDB formatted information
       input_files
          existing_ligand_file_list= None You can enter a list of PDB files with
                                     ligands you have already fit. These will be
                                     used to exclude that region from
                                     consideration.
          ligand_start= None LigandFit will attempt to put your ligand
                        superimposing on ligand_start if supplied. This must have
                        some of the same atoms as your ligand, but does not have
                        to have all of them.
          ncs_in= None You can supply a file with NCS information for use with
                  ligands_from_ncs
          input_ligand_compare_file= None If you enter a PDB file with a ligand in
                                     it, the coordinates of the newly-built ligand
                                     will be compared with the coordinates in this
                                     file.
          cif_def_file_list= None You can supply cif files for real-space
                             refinement after fitting
          refinement_file= None You can supply a file for full refinement
                           containing F/I SIGF/SIGI FreeR_flag If you supply this
                           file then after real-space refinement a round of full
                           refinement will be carried out with phenix.refine
          fobs_labels= None Labels for Fobs SigFobs or Iobs SigIobs for
                       refinement_file... same format as for phenix.refine
          r_free_label= None Label for FreeR_flag in refinement_file...same format
                        as for phenix.refine
       search_parameters
          conformers= 1 Enter how many conformers to create. If greater than 1,
                      then ELBOW will always be used to generate them. If 1 then
                      ELBOW will be used if a PDB file is not specified. These
                      conformers are used to identify allowed torsion angles for
                      your ligand. The alternative is to use the empirical rules
                      in RESOLVE. ELBOW takes longer but is more accurate.
          group_search= 0 Enter the ID number of the group from the ligand to use
                        to seed the search for conformations
          ligand_cc_min= 0.75 Enter the minimum correlation coefficient of the
                         ligand to the map to quit searching for more
                         conformations
          ligand_completeness_min= 1 Enter the minimum completeness of the ligand
                                   to the map to quit searching for more
                                   conformations
          local_search= True If local_search is True then, only the region within
                        search_dist of the point in the map with the highest local
                        rmsd will be searched in the FFT search for fragments
          search_dist= 10 If local_search is True then, only the region within
                       this distance of the point in the map with the highest
                       local rmsd will be searched in the FFT search for fragments
          use_cc_local= False You can specify the use of a local correlation
                        coefficient for scoring ligand fits to the map. If you do
                        not do this, then the region over which the ligand is
                        scored are all points within 2.5 A of the atoms in the
                        ligand. If you do specify use_cc_local, then the region
                        over which the ligand is scored are all these points, plus
                        all the contingous points that have density greater than
                        0.5 * sigma .
          ligands_from_ncs= False You can try to use ncs (from your partial model
                            file or from your ncs_in file) along with any ligands
                            already found to place additional copies of your
                            ligand. Only applicable if there is one type of
                            ligand.
          max_ligands_from_ncs= 1 You can specify how many of the ligands already
                                found to consider using NCS (usually 1)
          n_group_search= 3 Enter the number of different fragments of the ligand
                          that will be looked for in FFT search of the map
          n_indiv_tries_max= 10 If 0 is specified, all fragments are searched at
                             once otherwise all are first searched at once then
                             individually up to the number specified
          n_indiv_tries_min= 5 If 0 is specified, all placements of a fragment are
                             tested at once otherwise all are first tested at once
                             then individually up to the number specified
          number_of_ligands= 1 Number of copies of the ligand expected in the
                             asymmetric unit
          offsets_list= 7 53 29 You can specify an offset for the orientation of
                        the templates in searching for ligands. This is used in
                        generating diversity in models.
          refine_ligand= True You can carry out real-space refinement on the
                         ligand after fitting
          ligand_occupancy= 1.0 You can set the initial occupancy of the ligand
          real_space_target_weight= 10. You can carry change the weight on the
                                    real-space term in real-space refinement on
                                    the ligand after fitting
          fitting Parameters for tracing ligand
             delta_phi_ligand= 40 Specify the angle (degrees) between successive
                               tries in FFT search for fragments
             fit_phi_inc= 20 Specify the angle (degrees) between rotations around
                          bonds
             fit_phi_range= -180 180 Range of bond rotation angles to search
       search_target
          ligand_near_chain= None You can specify where to search for the ligand
                             either with search_center or with ligand_near_res and
                             ligand_near_chain. If you set
                             ligand_near_chain="None" or leave it blank
                             or do not set it, then all chains will be included.
                             The keywords ligand_near_res and ligand_near_chain
                             refer to residue/chain in the file defined by
                             input_partial_model_file (or model if running from
                             command line).
          ligand_near_res= None You can specify where to search for the ligand
                           either with search_center or with ligand_near_res and
                           ligand_near_chain The keywords ligand_near_res and
                           ligand_near_chain refer to residue/chain in the file
                           defined by input_partial_model_file (or model if
                           running from command line).
          ligand_near_pdb= None You can specify where LigandFit should look for
                           your ligands by providing a PDB file containing one or
                           more copies of the ligand. If you want you can provide
                           a PDB file with ligand+ macromolecule and specify the
                           ligand name with name_of_ligand_near_pdb.
          name_of_ligand_near_pdb= None You can specify where LigandFit should
                                   look for your ligands by providing a PDB file
                                   containing one or more copies of the ligand. If
                                   you want you can provide a PDB file with
                                   ligand+ macromolecule and specify the ligand
                                   name with name_of_ligand_near_pdb.
          search_center= 0.0 0.0 0.0 Enter coordinates for center of search region
                         (ignored if [0.,0.,0.])
       general
          extend_try_list= True You can fill out the list of parallel jobs to
                           match the number of jobs you want to run at one time,
                           as specified with nbatch.
          ligand_id= None You can specify an integer value for the ID of a
                     ligand... This number will be added to whatever residue
                     number the ligand search model in input_lig_file has. The
                     keyword is only valid if a single copy of the ligand is to be
                     found.
          nbatch= 5 You can specify the number of processors to use (nproc) and
                  the number of batches to divide the data into for parallel jobs.
                  Normally you will set nproc to the number of processors
                  available and leave nbatch alone. If you leave nbatch as None it
                  will be set automatically, with a value depending on the Wizard.
                  This is recommended. The value of nbatch can affect the results
                  that you get, as the jobs are not split into exact replicates,
                  but are rather run with different random numbers. If you want to
                  get the same results, keep the same value of nbatch.
          nproc= 1 You can specify the number of processors to use (nproc) and the
                 number of batches to divide the data into for parallel jobs.
                 Normally you will set nproc to the number of processors available
                 and leave nbatch alone. If you leave nbatch as None it will be
                 set automatically, with a value depending on the Wizard. This is
                 recommended. The value of nbatch can affect the results that you
                 get, as the jobs are not split into exact replicates, but are
                 rather run with different random numbers. If you want to get the
                 same results, keep the same value of nbatch. If you set
                 nproc=Auto and your machine has n processors, then it will use
                 n-1 processors, or 1 if only 1 is available
          resolve_command_list= None Commands for resolve. One per line in the
                                form: keyword value value can be optional
                                Examples: coarse_grid resolution 200 2.0 hklin
                                test.mtz NOTE: for command-line usage you need to
                                enclose the whole set of commands in double quotes
                                (") and each individual command in single
                                quotes (') like this:
                                resolve_command_list="'no_build' 'b_overall
                                23' "
          coot_name= "coot" If your version of coot is called something else, then
                     you can specify that here.
          i_ran_seed= 72432 Random seed (positive integer) for model-building and
                      simulated annealing refinement
          raise_sorry= False You can have any failure end with a Sorry instead of
                       simply printout to the screen
          background= True When you specify nproc=nn, you can run the jobs in
                      background (default if nproc is greater than 1) or
                      foreground (default if nproc=1). If you set run_command=qsub
                      (or otherwise submit to a batch queue), then you should set
                      background=False, so that the batch queue can keep track of
                      your runs. There is no need to use background=True in this
                      case because all the runs go as controlled by your batch
                      system. If you use run_command='sh ' (or similar, sh is
                      default) then normally you will use background=True so that
                      all the jobs run simultaneously.
          check_wait_time= 1.0 You can specify the length of time (seconds) to
                           wait between checking for subprocesses to end
          max_wait_time= 1.0 You can specify the length of time (seconds) to wait
                         when looking for a file. If you have a cluster where jobs
                         do not start right away you may need a longer time to
                         wait. The symptom of too short a wait time is 'File not
                         found'
          wait_between_submit_time= 1.0 You can specify the length of time
                                    (seconds) to wait between each job that is
                                    submitted when running sub-processes. This can
                                    be helpful on NFS-mounted systems when running
                                    with multiple processors to avoid file
                                    conflicts. The symptom of too short a
                                    wait_between_submit_time is File exists:....
          cache_resolve_libs= True Use caching of resolve libraries to speed up
                              resolve
          resolve_size= 12 Size for solve/resolve
                        ("","_giant",
                        "_huge","_extra_huge" or a number
                        where 12=giant 18=huge
          check_run_command= False You can have the wizard check your run command
                             at startup
          run_command= "sh " When you specify nproc=nn, you can run the
                       subprocesses as jobs in background with sh (default) or
                       submit them to a queue with the command of your choice
                       (i.e., qsub ). If you have a multi-processor machine, use
                       sh. If you have a cluster, use qsub or the equivalent
                       command for your system. NOTE: If you set run_command=qsub
                       (or otherwise submit to a batch queue), then you should set
                       background=False, so that the batch queue can keep track of
                       your runs. There is no need to use background=True in this
                       case because all the runs go as controlled by your batch
                       system. If nproc is greater than 1 and you use
                       run_command='sh '(or similar, sh is default) then normally
                       you will use background=True so that all the jobs run
                       simultaneously.
          queue_commands= None You can add any commands that need to be run for
                          your queueing system. These are written before any other
                          commands in the file that is submitted to your queueing
                          system. For example on a PBS system you might say:
                          queue_commands='#PBS -N mr_rosetta' queue_commands='#PBS
                          -j oe' queue_commands='#PBS -l walltime=03:00:00'
                          queue_commands='#PBS -l nodes=1:ppn=1' NOTE: you can put
                          in the characters '' in any queue_commands line and this
                          will be replaced by a string of characters based on the
                          path to the run directory. The first character and last
                          two characters of each part of the path will be
                          included, separated by '_',up to 15 characters. For
                          example
                          'test_autobuild/WORK_5/AutoBuild_run_1_/TEMP0/RUN_1'
                          would be represented by: 'tld_W_5_A1__TP0_1'
          condor_universe= vanilla The universe for condor is usually vanilla.
                           However you might need to set it to local for your
                           cluster
          add_double_quotes_in_condor= True You might need to turn on or off
                                       double quotes in condor job submission
                                       scripts. These are already default
                                       elsewhere but may interfere with condor
                                       paths.
          condor= None Specifies if the group_run_command is submitting a job to a
                  condor cluster. Set by default to True if
                  group_run_command=condor_submit, otherwise False. For condor job
                  submission mr_rosetta uses a customized script with condor
                  commands. Also uses one_subprocess_level=True
          last_process_is_local= True If true, run the last process in a group in
                                 background with sh as part of the job that is
                                 submitting jobs. This prevents having the job
                                 that is submitting jobs sit and wait for all the
                                 others while doing nothing
          skip_r_factor= False You can skip R-factor calculation if refinement is
                         not done and maps_only=True
          skip_xtriage= False You can bypass xtriage if you want. This will
                        prevent you from applying anisotropy corrections, however.
          base_path= None You can specify the base path for files (default is
                     current working directory)
          temp_dir= None Define a temporary directory (it must exist)
          clean_up= False At the end of the entire run the TEMP directories will
                    be removed if clean_up is True. The default is yes, delete
                    these directories. If you want to remove them after your run
                    is finished use a command like "phenix.autobuild run=1
                    clean_up=True" Files listed in keep_files will not be
                    deleted
          print_citations= True Print citations at end of run
          solution_output_pickle_file= None At end of run, write solutions to this
                                       file in output directory if defined
          title= None Enter any text you like to help identify what you did in
                 this run
          top_output_dir= None This is used in subprocess calls of wizards and to
                          tell the Wizard where to look for the STOPWIZARD file.
          wizard_directory_number= None This is used by the GUI to define the run
                                   number for Wizards. It is the same as
                                   desired_run_number NOTE: this value can only be
                                   specified on the command line, as the directory
                                   number is set before parameters files are read.
          verbose= False Command files and other verbose output will be printed
          extra_verbose= False Facts and possible commands will be printed every
                         cycle if True
          debug= False You can have the wizard stop with error messages about the
                 code if you use debug. Additionally the output goes to the
                 terminal if you specify "debug=True"
          require_nonzero= True Require non-zero values in data columns to
                           consider reading in.
          remove_path_word_list= None List of words identifying paths to remove
                                 from PATH These can be used to shorten your PATH.
                                 For example... cns ccp4 coot would remove all
                                 paths containing these words except those also
                                 containing phenix. Capitalization is ignored.
          fill= False Fill in all missing reflections to resolution res_fill.
                Applies to density modified maps. See also filled_2fofc_maps in
                autobuild.
          res_fill= None Resolution for filling in missing data (default = highest
                    resolution of any datafile). Only applies to density modified
                    maps. Default is fill to high resolution of data. Ignored if
                    fill=False
          check_only= False Just read in and check initial parameters. Not for
                      general use
          keep_files= ligandfit*.pdb List of files that are not to be cleaned up.
                      wildcards permitted
       display
          number_of_solutions_to_display= None Number of solutions to put on
                                          screen and to write out
          solution_to_display= 1 Solution number of the solution to display and
                               write out ( use 0 to let the wizard display the top
                               solution)
       run_control
          ignore_blanks= None ignore_blanks allows you to have a command-line
                         keyword with a blank value like
                         "input_lig_file_list="
          stop= None You can stop the current wizard with "stopwizard"
                or "stop". If you type "phenix.autobuild run=3
                stop" then this will stop run 3 of autobuild.
          display_facts= None Set display_facts to True and optionally
                         run=[run-number] to display the facts for run run-number.
                         If you just say display_facts then the facts for the
                         highest-numbered existing run will be shown.
          display_summary= None Set display_summary to True and optionally
                           run=[run-number] to show the summary for run
                           run-number. If you just say display_summary then the
                           summary for the highest-numbered existing run will be
                           shown.
          carry_on= None Set carry_on to True to carry on with highest-numbered
                    run from where you left off.
          run= None Set run to n to continue with run n where you left off.
          copy_run= None Set copy_run to n to copy run n to a new run and continue
                    where you left off.
          display_runs= None List all runs for this wizard.
          delete_runs= None List runs to delete: 1 2 3-5 9:12
          display_labels= None display_labels=test.mtz will list all the labels
                          that identify data in test.mtz. You can use the label
                          strings that are produced in AutoSol to identify which
                          data to use from a datafile like this:
                          peak.data="F+ SIGF+ F- SIGF-" # the entire
                          string in quotes counts here You can use the individual
                          labels from these strings as identifiers for data
                          columns in AutoSol and AutoBuild like this:
                          input_refinement_labels="FP SIGFP FreeR_flags"
                          # each individual label counts
          dry_run= False Just read in and check parameter names
          params_only= False Just read in and return parameter defaults
          display_all= False Just read in and display parameter defaults
          coot= None Not presently applicable for ligandfit
       special_keywords
          write_run_directory_to_file= None Writes the full name of a run
                                       directory to the specified file. This can
                                       be used as a call-back to tell a script
                                       where the output is going to go.
       non_user_parameters These are obsolete parameters and parameters that the
                           wizards use to communicate among themselves. Not
                           normally for general use.
          gui_output_dir= None Used only by the GUI
          sg= None Obsolete. Use space_group instead
          get_lig_volume= False You can ask to get the volume of the ligand and to
                          then stop
          input_data_file= None Not normally used. Use "data=" instead
          input_lig_file= None Not normally used. Use "ligand=" instead.
          ligand_code= None Not normally used. Use "ligand=" instead.
          input_partial_model_file= None Not normally used. Use "model="
                                    instead
          cif_already_generated= False You can specify that the ligand cif file is
                                 already generated